If you use spray paint, DO NOT use the paint that dries to the touch in less than a hour. You will not be happy with the results. It dries too fast to allow the paint to flow together.
Yes stain will bless thru paint. I have some that I stained with an alcohol based red stain and tried covering it up with some white paint, and it looked great till about a week later the red started to bleed thru the white, so yes it does happen.
Just figure where you want to stop the stain and start your crown and put a pencil mark there. And carefully stain up to it. I use a shotgun cleaning patch to do my staining. They allow me to get in real close in a neat fashion.